Inferring SARS-CoV-2 variant within-host kinetics

SARS-CoV-2 variants are causing epidemic rebounds in many countries. By analyzing longitudinal cycle threshold (Ct) values from screening tests in the general population and hospitals, we find that infections caused by variant lineages have higher peak viral load than wild type lineages and, for the B.1.1.7 lineage, have a longer infectious period duration. Linking within-host kinetics to transmission data suggests that infections caused by variants have higher transmission potentials and that their epidemiological fitness may depend on the demography of the host population.